To increase the resilience of agroecosystems, and allow for sustainable economic reactivation, it is vital that the introduction of sustainable measures - particularly in agriculture – is advanced via an integrated management approach such as the Resource Nexus. An essential aspect of this approach is to optimise the efficiency of ecosystems and resources in conjunction with environmentally friendly economic growth. Colombia has experienced the impact of armed conflict over many years, while geographic regions have been shaped by environmental conflicts; resulting in vulnerable areas suffering from land and population inequalities that also translate into wicked planning for resilient food systems. This paper addresses a double challenge: the improvement of natural resources management and reducing the population's vulnerability in line with the principles of inclusion and gender equity. The paper developed a methodology to identify those productive regions that require improved management at the landscape level, which could benefit under the main framework of the water-energy-food Nexus. It also provides evidence of the value of the science-policy interface to ensure increased social equity, economic growth, and the conservation of resources. A geographic information system approach has been utilised to spatially evaluate the effects of land-use change, ecosystem services provision, and the impacts of climate change at the municipality scale of productive agricultural regions. The objectives of this research were to: (i) evaluate the impact of climate change and anthropogenic activities on natural resources, (ii) assess productive landscape fragmentation due to the overuse of resources, and (iii) consider ecosystem services planning as an operational methodology for municipality ecosystem-based management. The study results show a decrease in the natural Andean Forest, coupled with an increase in agricultural fields over the past 35 years, and a decrease in freshwater availability in the last decade. The expansion trend of the agricultural frontier into the protected areas is also highlighted.